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In this video, the lecturer says:

You see that phenylalanine is probably still phenylalanine because only one percent of amino acids have changed so roughly 99 percent of the time, phenylalanine is still phenylalanine. Now why is it not exactly 99 percent? Because it’s one percent for all 20 amino acids so some are greater than 99 percent and some are less than 99 percent. It averages out to 99 percent.

What on earth does he mean by this? I either do not have the background knowledge or am not thinking hard enough, or I need this to be explained in a way that is more understandable.

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It means that the 99% of conservation of amino acids is just a mean value for all the amino acids. That there can be amino acids that are less conserved and some that are more conserved.

So from the 21 basic amino acids, arginine is more conserved than lysine in those alignments. But in general they are conserved the 99% of times.

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